In order to investigate the effect of microstructure of PEMFC porous layers on the liquid water behavior, liquid water accumulation and discharge behavior in the operating PEMFC was visualized by soft X-ray radiography. The utilization of low energy X-ray made it possible to detect the liquid water behavior in the porous layers with high temporal and spatial resolution, and the cross-sectional imaging can resolve the each components of the PEMFC. The visualization results showed that the liquid water distribution in the carbon paper and the carbon cloth GDL was completely different. The liquid water in the carbon cloth GDL concentrates at the weaves of fiber bundle and was effectively discharged to the channel. In addition, to investigate the effect of the network of pores in more detail, stereo imaging of the liquid water evaporation process from the carbon paper GDL was carried out. These visualization results suggested that the microstructure of the PEMFC porous layers strongly affect the liquid water behavior in the PEMFC.